Custom placement of trees has nothing to do with the tree generator or tree library used. We simply cannot use SpeedTree trees with the amounts this world requires, so that's why we need the generator optimized for it. You can still have a few trees as models though.
Custom placement will be done as everything else - by defining vector shapes that modify the underlying model that's supposed to generate the basic tree coverage from available data (real-world forest coverage, climatic models). The shapes can alter it by cutting or putting the trees, changing the type and other parameters etc.
Note that making a MMO work on a single world the size of Earth isn't one of the problems we are solving in any near term. Making a MMO brings a lot more problems than making other types of games, and OT still needs to address the basic needs that games/sims may have (also the ones you listed). There's a lot of games that could use OT as a world rendering engine, in singleplayer or with their own custom networking for multiplayer. OT initially won't provide its own networking as there's a wide array of game types, each having specific requirements, with their preferred networking libraries.
There's a reason why the big fish do the splitting, if it was easy it would be used already. But technically it's an orthogonal thing to the world rendering engine, it could (and perhaps should) be developed separately. Volunteers?